For the Flow Cytometry (FC) and Resistence (RES) data we will filter guides in 2 steps:
| Cell | Gene | Avg. Rep. Correlation | Avg. Variance | Avg.Avg.LFC | Guides | Avg.LFC Variance | Dip.Test.P-Val | Remove |
|---|---|---|---|---|---|---|---|---|
| MOLM-13 | CD15 | 0.9662890 | 0.0240898 | 0.4856672 | 384 | 0.6922808 | 0.0000 | FALSE |
| TF-1 | CD13 | 0.9570524 | 0.0646212 | 0.5501278 | 480 | 1.4466709 | 0.0000 | FALSE |
| MOLM-13 | CD33 | 0.9429190 | 0.0586406 | 1.8360495 | 192 | 0.9571894 | 0.9565 | FALSE |
| NB4 | CD13 | 0.9586049 | 0.0566933 | 0.7731802 | 480 | 1.2946018 | 0.6685 | TRUE |
| NB4 | CD33 | 0.9098274 | 0.1258232 | 1.5708943 | 192 | 1.2518799 | 0.9355 | TRUE |
Guides targetting CD13 are more variable in TF-1 cells, so we will get better seperation between good and bad guides
Lower technical replicate correlation of CD44 in NB4 is lower
Note: Replicates for FC data are technical, not experimental
Guides are highly variability if they have a variance greater than 3 standard deviations from the mean variability
Removed 10 guides*
| Gene | Avg.Rep.Correlation | Avg.Variance | Avg.Avg.LFC | Guides | Avg.LFC Variance | Dip.Test.P-Val | Remove |
|---|---|---|---|---|---|---|---|
| H2-K | 0.8211892 | 1.2035568 | 2.1761582 | 235 | 5.6704374 | 0.0040 | FALSE |
| CD45 | 0.8140521 | 1.2587999 | 1.1741811 | 584 | 5.6286802 | 0.0000 | FALSE |
| Cd5 | 0.7660277 | 2.0192704 | 1.0007152 | 423 | 6.9193161 | 0.0005 | FALSE |
| Cd43 | 0.7573723 | 1.5938866 | 0.5684481 | 637 | 5.2267523 | 0.0000 | FALSE |
| Thy1 | 0.7461000 | 2.0896311 | 0.7131360 | 363 | 6.4481478 | 0.0005 | FALSE |
| Cd28 | 0.5857841 | 6.8655039 | -1.0380493 | 438 | 10.8284672 | 0.4175 | FALSE |
| Cd53 | 0.5657920 | 0.1380933 | 0.4814790 | 238 | 0.2021161 | 0.5420 | TRUE |
| Cd3e | 0.4469605 | 2.7745785 | 0.2972853 | 260 | 2.6989556 | 0.9465 | TRUE |
| Cd2 | 0.1999299 | 0.2130592 | 0.1159250 | 191 | 0.0885697 | 0.8120 | TRUE |
Remove highly variable guides (variance of LFC’s 3 sd from mean)
| Drug | Gene | Avg. Rep. Correlation | Avg. Variance | Avg.Avg.LFC | Guides | Avg.LFC Variance | Dip.Test.P-Val | Remove |
|---|---|---|---|---|---|---|---|---|
| 6TG | HPRT1 | 0.9296532 | 0.5917359 | 3.6539692 | 64 | 7.5110608 | 0.9915945 | FALSE |
| AZD | MED12 | 0.8758470 | 0.4875722 | 0.6236769 | 956 | 3.5307290 | 0.9935129 | FALSE |
| AZD | TADA1 | 0.8184488 | 0.6957460 | -0.6849490 | 111 | 3.1061818 | 0.0574928 | FALSE |
| AZD | TADA2B | 0.7575317 | 0.6708192 | -0.1506191 | 201 | 2.1925174 | 0.9914553 | FALSE |
| AZD | CCDC101 | 0.7042762 | 0.9569480 | -0.2300276 | 160 | 2.4852626 | 0.9866788 | FALSE |
| PLX | NF2 | 0.6519871 | 1.4997459 | -0.0615335 | 226 | 3.1726561 | 0.8529861 | FALSE |
| PLX | NF1 | 0.5680280 | 1.8320517 | -0.9834906 | 745 | 2.8341151 | 0.0414965 | FALSE |
| PLX | MED12 | 0.7805298 | 0.7922638 | -0.5966506 | 956 | 2.9941566 | 0.8994090 | TRUE |
| PLX | CUL3 | 0.4344678 | 2.9605273 | -0.6183203 | 155 | 2.9995941 | 0.6150521 | TRUE |
| 6TG | PMS2 | 0.2618040 | 1.1758838 | -4.1004333 | 262 | 0.6980747 | 0.9928136 | TRUE |
| 6TG | MSH2 | 0.2541437 | 1.8882252 | -4.2050059 | 224 | 1.1143426 | 0.9912448 | TRUE |
| 6TG | MSH6 | 0.1981200 | 1.4471243 | -4.2796887 | 432 | 0.7176871 | 0.9909761 | TRUE |
| 6TG | MLH1 | 0.1093879 | 1.3699372 | -4.3180802 | 256 | 0.5058294 | 0.8154171 | TRUE |
Remove highly variable guides (variance of LFC’s 3 sd from mean)
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